I have a complicated design that changes color to black when I try to make a compound path. All strokes are outlined, all parts are grouped. I am trying to use this design for a clipping mask.

The Compound Path>Make command is different from the Clipping Mask>Make command.

Compounding a complex number of paths into a single compound path will give the resulting object a single fill. This is probably why the entire group is turning black. A clipping mask is used to show/hide portions of a larger object. Are you trying to do that with the pattern object? Or are you trying to do something else, such as create a cut path to go around the pattern?